The drugs used to treat HIV are “substrates” or molecules that enzymes of
the HIV virus bind and act upon. The reverse transcriptase and the
protease are the two main enzymes that are the targets of anti-HIV drugs.
Resistance occurs when these enzymes evolve into a form that no longer
binds the drug.

The reverse transcriptase is the enzyme responsible for copying the RNA
which contains the genetic information of the virus. This enzyme binds the
nucleotide molecules, dATP, dCTP, dGTP, and dTTP, and adds them to the
newly synthesized DNA copy of the HIV genome. AZT, the first anti-AIDS
drug, has a structure similar to dTTP. But AZT has an azido group
consisting of three nitrogen atoms where dTTP has an OH. AZT can fit into
the active site of the reverse transcriptase. Thus AZT can be taken up by
the reverse transcriptase as if it was dTTP and AZT can be added to the new
stand of DNA that is being synthesized. But the nitrogen on the AZT acts
as a block to synthesis and no more nucleotides can be added to that
particular strand of DNA. Thus the strand is effectively dead.

Note, there are also cellular DNA polymerases that use dTTP to make DNA for
the cell. The cellular polymerases bind dTTP about 100 times better than
AZT, so the cell is relatively safe from AZT. How does this happen?

As mentioned above, nucleotides are substrates for the reverse
transcriptase. Substrates fit into enzymes like a hand fits into a glove.
Enzymes are proteins. Like all proteins, enzymes are composed of amino
acids and each enzyme is made of its own particular sequence of amino
acids. The reverse transcriptase and the cellular DNA polymerase have some
structural similarities, but their amino acid sequences are different. The
amino acid differences in the substrate binding sites affect the sites in
such a way that the reverse transcriptase binds and incorporates AZT more
that the cellular polymerase.

How does HIV evade anti-HIV drugs? After AZT treatment, one of the first
changes found in the HIV reverse transcriptase is that the amino acid
lysine at position 70 is changed to an arginine. Reverse transcriptase
with this change is 4 to 8 fold resistant to AZT. Then the threonine at
position 215 is often found changed into a tyrosine. This adds another 10
fold resistance, for a total 64 fold resistance. With changes in its amino
acid sequence, the reverse transcriptase evolves into a structure that
binds and functions with dTTP and rejects AZT.

How does HIV create the resistant forms of its enzymes? The reverse
transcriptase, the enzyme that copies the genome of HIV, is rather
inaccurate. It makes mistakes in the DNA at a rate of about 3x10-5 per
nucleotide. The HIV genome is about 10x10+3 nucleotides long, so 0.3
(about 1 in 3) will have a mutation. Every 3x10+4 viruses will give a
chance that each nucleotide will be mutated. An infected person may
produce 10x10+9 viruses a day, and that is enough to produce mutations at
every site, and many different combinations of mutations. And mutations in
the genes will be represented as changes in the enzymes the genes code for.
This way it can be seen that a reverse transcriptase with a resistance
mutation is bound to occur. Many mutated viruses will not be viable and
after treatment the level of viruses falls rapidly. However, with just
AZT, a resistant virus often appears within a year.

If two reverse transcriptase inhibitor drugs are given, the chance that the
combination of mutations needed to produce resistance to both drugs will
occur at the same time is proportionally smaller. Add an inhibitor to the
protease (another enzyme that HIV needs for its life cycle), and a mutation
in this enzyme also has to occur for the HIV to survive. This is called
“triple therapy” or “HAART” (highly active anti-retroviral therapy). HAART
can reduce the viral load to “undetectable” or below 20 viruses per ml.
HAART increases the health and adds many years of life to someone infected
with HIV, but even with this low level of virus they can still spread HIV
infection.

In the past it was hoped that reducing the HIV to low levels would
eventually eliminate the virus, but this hasn’t been found to happen. New
drugs like Fuzeon, a fusion inhibitor, have been approved and drugs are
being developed to block other targets. But they all interact with
proteins, and the problem of HIV developing resistance persists.